FMO DATABASE

FMODB ID: GNV31

Calculation Name: 3U4Z-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3U4Z

Chain ID: A

ChEMBL ID:

UniProt ID: D2CVN6

Base Structure: X-ray

Registration Date: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	109
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-905426.549788
FMO2-HF: Nuclear repulsion	860006.726264
FMO2-HF: Total energy	-45419.823524
FMO2-MP2: Total energy	-45552.964184

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:375:THR)

Summations of interaction energy for fragment #1(A:375:THR)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-7.72	-2.135	6.056	-3.976	-7.664	-0.021

Interaction energy analysis for fragmet #1(A:375:THR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.037 / q_NPA : -0.027

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	377	LEU	0	0.044	0.023	3.208	-1.248	1.193	0.167	-1.133	-1.474	-0.001
4	A	378	ILE	0	0.054	0.015	5.078	0.413	0.459	-0.001	-0.001	-0.044	0.000
5	A	379	SER	0	-0.007	-0.016	7.887	0.091	0.091	0.000	0.000	0.000	0.000
6	A	380	GLU	-1	-0.801	-0.905	6.944	-0.415	-0.415	0.000	0.000	0.000	0.000
7	A	381	VAL	0	0.013	0.015	6.445	0.255	0.255	0.000	0.000	0.000	0.000
8	A	382	LEU	0	0.056	0.026	9.127	0.123	0.123	0.000	0.000	0.000	0.000
9	A	383	LYS	1	0.892	0.930	12.194	0.178	0.178	0.000	0.000	0.000	0.000
10	A	384	THR	0	-0.058	-0.023	8.994	0.078	0.078	0.000	0.000	0.000	0.000
11	A	385	SER	0	0.005	0.005	12.065	0.028	0.028	0.000	0.000	0.000	0.000
12	A	386	LYS	1	0.827	0.925	6.722	-0.891	-0.891	0.000	0.000	0.000	0.000
13	A	387	GLN	0	0.036	0.020	11.623	-0.020	-0.020	0.000	0.000	0.000	0.000
14	A	388	TYR	0	0.037	0.016	9.305	-0.056	-0.056	0.000	0.000	0.000	0.000
15	A	389	LEU	0	-0.019	-0.014	5.799	0.012	0.012	0.000	0.000	0.000	0.000
16	A	390	SER	0	0.037	0.028	2.643	-1.426	-0.617	0.270	-0.344	-0.736	0.001
17	A	391	VAL	0	-0.011	0.004	2.195	-3.109	-1.198	2.773	-2.381	-2.303	-0.021
18	A	392	LEU	0	-0.004	0.019	2.346	1.234	0.304	2.777	0.266	-2.112	-0.003
19	A	393	ALA	0	-0.011	-0.012	3.670	-0.903	-0.898	0.005	0.107	-0.117	0.000
20	A	394	GLN	0	-0.012	-0.013	7.166	0.079	0.079	0.000	0.000	0.000	0.000
21	A	395	VAL	0	0.005	0.012	10.786	0.016	0.016	0.000	0.000	0.000	0.000
22	A	396	VAL	0	0.002	0.001	13.591	-0.043	-0.043	0.000	0.000	0.000	0.000
23	A	397	ASP	-1	-0.843	-0.913	16.430	0.135	0.135	0.000	0.000	0.000	0.000
24	A	398	ILE	0	-0.018	-0.004	17.541	0.048	0.048	0.000	0.000	0.000	0.000
25	A	399	GLN	0	-0.029	-0.012	19.753	-0.025	-0.025	0.000	0.000	0.000	0.000
26	A	400	SER	0	-0.001	-0.013	21.879	0.026	0.026	0.000	0.000	0.000	0.000
27	A	401	SER	0	0.002	-0.008	23.616	-0.007	-0.007	0.000	0.000	0.000	0.000
28	A	402	ASP	-1	-0.878	-0.936	25.951	0.169	0.169	0.000	0.000	0.000	0.000
29	A	403	LYS	1	0.912	0.957	25.811	-0.162	-0.162	0.000	0.000	0.000	0.000
30	A	404	ASN	0	0.021	-0.004	21.851	0.039	0.039	0.000	0.000	0.000	0.000
31	A	405	ILE	0	-0.015	0.023	18.128	-0.022	-0.022	0.000	0.000	0.000	0.000
32	A	406	ARG	1	0.890	0.933	18.124	-0.190	-0.190	0.000	0.000	0.000	0.000
33	A	407	LEU	0	0.024	0.011	13.413	-0.021	-0.021	0.000	0.000	0.000	0.000
34	A	408	LYS	1	0.899	0.957	14.946	-0.139	-0.139	0.000	0.000	0.000	0.000
35	A	409	ILE	0	-0.043	-0.029	7.946	0.015	0.015	0.000	0.000	0.000	0.000
36	A	410	CYS	0	0.045	0.013	11.097	-0.051	-0.051	0.000	0.000	0.000	0.000
37	A	411	ASP	-1	-0.729	-0.834	6.999	-0.900	-0.900	0.000	0.000	0.000	0.000
38	A	412	ASN	0	0.012	-0.005	8.832	0.109	0.109	0.000	0.000	0.000	0.000
39	A	413	SER	0	-0.101	-0.059	7.935	0.029	0.029	0.000	0.000	0.000	0.000
40	A	414	CYS	0	-0.043	-0.016	10.075	0.071	0.071	0.000	0.000	0.000	0.000
41	A	415	ASN	0	0.015	0.002	12.614	0.014	0.014	0.000	0.000	0.000	0.000
42	A	416	GLN	0	0.000	0.000	14.388	0.012	0.012	0.000	0.000	0.000	0.000
43	A	417	GLU	-1	-0.858	-0.914	13.405	0.080	0.080	0.000	0.000	0.000	0.000
44	A	418	LEU	0	-0.029	-0.013	9.160	0.002	0.002	0.000	0.000	0.000	0.000
45	A	419	LYN	0	0.063	0.057	12.951	0.034	0.034	0.000	0.000	0.000	0.000
46	A	420	VAL	0	-0.005	-0.003	10.757	0.049	0.049	0.000	0.000	0.000	0.000
47	A	421	VAL	0	-0.004	-0.002	13.955	-0.058	-0.058	0.000	0.000	0.000	0.000
48	A	422	ILE	0	0.005	-0.006	13.952	0.066	0.066	0.000	0.000	0.000	0.000
49	A	423	PHE	0	0.035	-0.005	17.041	-0.047	-0.047	0.000	0.000	0.000	0.000
50	A	424	PRO	0	0.008	-0.027	19.981	0.026	0.026	0.000	0.000	0.000	0.000
51	A	425	ASP	-1	-0.870	-0.923	20.686	0.354	0.354	0.000	0.000	0.000	0.000
52	A	426	LEU	0	0.023	0.013	13.695	-0.011	-0.011	0.000	0.000	0.000	0.000
53	A	427	CYS	0	-0.084	-0.038	18.367	-0.021	-0.021	0.000	0.000	0.000	0.000
54	A	428	TYR	0	-0.015	-0.016	20.025	-0.032	-0.032	0.000	0.000	0.000	0.000
55	A	429	GLU	-1	-0.909	-0.943	17.160	0.425	0.425	0.000	0.000	0.000	0.000
56	A	430	TRP	0	-0.023	-0.040	13.854	0.007	0.007	0.000	0.000	0.000	0.000
57	A	431	ARG	1	0.835	0.923	19.095	-0.215	-0.215	0.000	0.000	0.000	0.000
58	A	432	ASP	-1	-0.926	-0.966	22.023	0.200	0.200	0.000	0.000	0.000	0.000
59	A	433	LYS	1	0.903	0.983	16.453	-0.352	-0.352	0.000	0.000	0.000	0.000
60	A	434	PHE	0	0.012	0.001	12.870	-0.006	-0.006	0.000	0.000	0.000	0.000
61	A	435	SER	0	-0.021	-0.013	16.317	-0.053	-0.053	0.000	0.000	0.000	0.000
62	A	436	ILE	0	0.023	0.002	16.035	0.025	0.025	0.000	0.000	0.000	0.000
63	A	437	ASN	0	-0.030	-0.028	15.016	-0.019	-0.019	0.000	0.000	0.000	0.000
64	A	438	LYS	1	0.802	0.910	13.450	-0.230	-0.230	0.000	0.000	0.000	0.000
65	A	439	TRP	0	-0.017	-0.010	6.953	0.032	0.032	0.000	0.000	0.000	0.000
66	A	440	TYR	0	-0.002	-0.012	8.417	-0.084	-0.084	0.000	0.000	0.000	0.000
67	A	441	TYR	0	0.016	0.002	3.280	-1.867	-0.564	0.065	-0.490	-0.878	0.003
68	A	442	PHE	0	-0.006	0.002	5.801	-0.736	-0.736	0.000	0.000	0.000	0.000
69	A	443	ASN	0	-0.043	-0.046	5.427	1.792	1.792	0.000	0.000	0.000	0.000
70	A	444	GLU	-1	-0.871	-0.953	6.439	0.756	0.756	0.000	0.000	0.000	0.000
71	A	445	PHE	0	-0.002	0.018	8.029	-0.453	-0.453	0.000	0.000	0.000	0.000
72	A	446	VAL	0	-0.033	-0.023	9.772	0.047	0.047	0.000	0.000	0.000	0.000
73	A	447	ARG	1	0.864	0.935	10.973	-0.361	-0.361	0.000	0.000	0.000	0.000
74	A	448	GLN	0	-0.007	-0.003	12.780	-0.047	-0.047	0.000	0.000	0.000	0.000
75	A	449	ILE	0	0.014	0.001	16.315	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	450	TYR	0	-0.069	-0.044	18.676	-0.008	-0.008	0.000	0.000	0.000	0.000
77	A	451	ASN	0	-0.027	-0.018	21.635	-0.010	-0.010	0.000	0.000	0.000	0.000
78	A	452	ASP	-1	-0.916	-0.946	22.216	0.086	0.086	0.000	0.000	0.000	0.000
79	A	453	GLU	-1	-0.940	-0.954	18.658	0.092	0.092	0.000	0.000	0.000	0.000
80	A	454	VAL	0	-0.063	-0.038	13.161	0.034	0.034	0.000	0.000	0.000	0.000
81	A	455	GLN	0	-0.002	-0.015	13.825	-0.044	-0.044	0.000	0.000	0.000	0.000
82	A	456	LEU	0	-0.025	-0.005	8.200	0.049	0.049	0.000	0.000	0.000	0.000
83	A	457	LYS	1	0.820	0.919	12.633	-0.566	-0.566	0.000	0.000	0.000	0.000
84	A	458	ASN	0	0.074	0.032	13.447	0.163	0.163	0.000	0.000	0.000	0.000
85	A	459	ASN	0	-0.024	-0.019	14.139	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	460	ILE	0	0.041	0.020	15.501	0.046	0.046	0.000	0.000	0.000	0.000
87	A	461	HIS	0	0.022	0.017	13.294	-0.040	-0.040	0.000	0.000	0.000	0.000
88	A	462	SER	0	-0.066	-0.030	11.486	0.054	0.054	0.000	0.000	0.000	0.000
89	A	463	SER	0	0.009	0.001	10.483	-0.129	-0.129	0.000	0.000	0.000	0.000
90	A	464	ILE	0	0.011	0.004	9.698	0.310	0.310	0.000	0.000	0.000	0.000
91	A	465	LYS	1	0.952	0.979	8.751	-0.759	-0.759	0.000	0.000	0.000	0.000
92	A	466	GLU	-1	-0.789	-0.874	9.354	0.427	0.427	0.000	0.000	0.000	0.000
93	A	467	SER	0	-0.021	-0.004	7.839	-0.026	-0.026	0.000	0.000	0.000	0.000
94	A	468	ASP	-1	-0.871	-0.934	9.578	0.028	0.028	0.000	0.000	0.000	0.000
95	A	469	ASP	-1	-0.909	-0.933	10.887	-0.344	-0.344	0.000	0.000	0.000	0.000
96	A	470	GLN	0	-0.019	-0.005	11.113	-0.055	-0.055	0.000	0.000	0.000	0.000
97	A	471	ARG	1	0.846	0.903	13.287	0.215	0.215	0.000	0.000	0.000	0.000
98	A	472	LYS	1	0.989	0.995	16.709	-0.026	-0.026	0.000	0.000	0.000	0.000
99	A	473	VAL	0	0.024	0.014	18.845	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	474	ILE	0	-0.034	-0.021	21.024	0.014	0.014	0.000	0.000	0.000	0.000
101	A	475	THR	0	-0.002	0.005	24.118	-0.011	-0.011	0.000	0.000	0.000	0.000
102	A	476	TYR	0	0.005	0.000	26.177	0.012	0.012	0.000	0.000	0.000	0.000
103	A	477	ASN	0	-0.012	-0.005	26.701	-0.012	-0.012	0.000	0.000	0.000	0.000
104	A	478	GLN	0	-0.027	-0.013	30.683	0.006	0.006	0.000	0.000	0.000	0.000
105	A	479	GLU	-1	-0.858	-0.928	34.468	-0.018	-0.018	0.000	0.000	0.000	0.000
106	A	480	GLN	0	0.033	0.002	32.448	-0.003	-0.003	0.000	0.000	0.000	0.000
107	A	481	GLY	0	-0.001	0.005	37.406	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	482	VAL	0	-0.053	-0.026	40.170	0.001	0.001	0.000	0.000	0.000	0.000
109	A	483	PHE	0	-0.063	-0.016	36.511	-0.002	-0.002	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:375:THR)